Figure 1.
Implicit Solvent Potentials of Mean Force for representative residue pairs.
Plots show interaction energy vs. distance, at distance intervals of 0.25 Å, for a pair of residues in a given orientation. Distance refers to the P-C distance between the phosphate atom and the terminal carbon on Arg (coplanar), or the N-O distance (collinear).
Figure 2.
Snapshots from molecular dynamics simulation of two tripeptide systems.
Interactions appearing at high frequency are (a) bidentate hydrogen bond in Arg-Gly-pTyr(−2) and (b) single hydrogen bond in Lys-Gly-pTyr(−2). Hydrogen Bonds are indicated by dotted yellow lines.
Figure 3.
Percentage of Glu, pSer, pTyr and sTyr residues showing a given number of hydrogen bonds.
Residues were drawn from all structures in the Protein Databank containing a pSer, pTyr, or sTyr residue. For Glu, residues were taken from the set of structures containing a pSer residue.
Table 1.
Hydrogen Bond Occupancies in Molecular Dynamics Simulation of Tripeptide Systems.
Table 2.
Hydrogen Bonding Energies in kcal/mol computed using Implicit Solvation Molecular Mechanics on residue pairs.
Table 3.
Characterization of Hydrogen Bonds to Glu, pSer, pTyr, and sTyr in Experimental Protein Structures.
Figure 4.
A comparison of electrostatic potentials for sTyr, pTyr(−1), and pTyr(−2).
Electrostatic potentials are shown at isosurfaces of +/−2 kTe. The protonated phosphate group of pTyr(−1) presents a shaped charge that can provide a stronger interaction with hydrogen bond donors than the more isotropic charge on the sTyr sulfate.